Unusual DNA conformations

Current Opinion in Structural Biology

Volumn 7, Issue 3, 1997, Pages 348-354

  Lebrun, Anne ^a   Lavery, Richard ^a  

^a France   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA;

ARTICLE; BASE PAIRING; COMPLEX FORMATION; DNA CONFORMATION; DNA DNA HYBRIDIZATION; PRIORITY JOURNAL;

EID: 0030965361     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80050-4     Document Type: Article

References (68)

1. 2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'deoxythymidine nucleotides. Nucleic Acids Res. 24:1996;951-961.
2. Ding D, Gryaznov SM, Lloyd DH, Chandrasekaran S, Yao S, Ratmeyer L, Pan Y, Wilson WD. An oligodeoxyribonucleotide N3'→P5' phosphoramidate duplex forms an A-type helix in solution. Nucleic Acids Res. 24:1996;354-360.
3. Aramini JM, Kalisch BW, Pon RT, Van de Sande JH, Germann MW. Structure of a DNA duplex that contains α-anomeric nucleotides and 3'-3' and 5'-5' phosphodiester linkages: coexistence of parallel and antiparallel DNA. Biochemistry. 35:1996;9355-9365.
4. Torres RA, Almarsson O, Bruice TC. Molecular mechanics calculations of the riboacetal internucleotide linkage in double and triple helices. Biochemistry. 93:1996;6875-6880.
5. Sahasrabudhe PV, Pon RT, Gmeiner WH. Solution structures of 5-fluorouracil-substituted DNA and RNA decamer duplexes. Biochemistry. 35:1996;13597-13608.
6. Moo MH, Van Meervelt L, Salisbury SA, Kong Thoo Lin P, Brown DM. Direct observation of two base-pairing modes of a cystosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis. J Mol Biol. 251:1995;665-673.
7. Eriksson M, Nielsen PE. Solution structure of a peptide nucleic acid - DNA duplex. Nat Struct Biol. 3:1996;410-413 A solution structure of a PNA - DNA duplex that adopts a conformation between the canonical A and B forms - in contrast to an earlier study of a PNA - RNA duplex that has an A-like conformation [68]. of special interest.
8. Betts L, Josey JA, Veal JM, Jordan SR. A nucleic acid triple helix formed by a peptide nucleic acid - DNA complex. Science. 270:1995;1838-1841 The authors present an X-ray structure for a triple helix with two PNA strands and one DNA strand that has become a very useful model for other groups working in this area. of outstanding interest.
9. Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE. Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 Å resolution. Nat Struct Biol. 4:1997;98-101 The crystal structure of a PNA - PNA duplex closely resembles the so-called 'P-helix' seen within the triplex presented in [8]. of outstanding interest of special interest.
10. Footer M, Egholm M, Kron S, Coull JM, Matsudaira P. Biochemical evidence that a D-loop is part of a four-stranded PNA - DNA bundle. Nickel-mediated cleavage of duplex DNA by a Gly-Gly-His Bis-PNA. Biochemistry. 35:1996;10673-10679.
11. Horton NC, Finzel BC. The structure of an RNA/DNA hybrid: substrate of the ribonuclease activity of HIV-1 reverse transcriptase. J Mol Biol. 264:1996;521-533.
12. Ban C, Ramakrishnan B, Sundaralingam M. A single 2′-hydroxyl group converts B-DNA to A-DNA. J Mol Biol. 236:1994;275-285.
13. Salazar M, Fedoroff OY, Reid BR. Structure of chimeric duplex junctions: solution conformation of the retroviral Okazaki-like fragment r(CCCA)d(AATGA)-d(TCATTTGGG) from Moloney Murine Leukemia virus. Biochemistry. 35:1996;8126-8135.
14. Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E. Solution structures of DNA duplexes containing a DNA-RNA hybrid region d(GG)r(AGAU)d(GAC)·d(GTCATCTCC) and d(GGAGA)r(UGAC)·d(GTCATCTCC). Biochemistry. 35:1996;4016-4025.
15. Fedoroff OY, Salazar M, Reid BR. Structural variation among retroviral primer-DNA junctions: solution structure of the HIV-1 (-)·strand Okazaki fragment r(GCCA)d(CTGC)·d(GCAGTGGC). Biochemistry. 35:1996;11070-11080.
16. Ivanov VI, Minchinenkova LE, Burckhardt G, Birch-Hirschfeld E, Fritzsche H, Zimmer C. The detection of B-form/A-form junction in a deoxyribonucleotide duplex. Biophys J. 71:1996;3344-3349.
17. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;87-92 Uracil-DNA glycosylase is able to extract a single nucleotide from within a DNA duplex causing only minor structural perturbation. The authors propose possible mechanisms that allow this enzyme to actively promote base-pair disruption. of outstanding interest.
18. 6 DNA methyltransferases requires different deformations of DNA. Proc Natl Acad Sci USA. 93:1996;7618-7622.
19. Cosman M, Hingerty BE, Luneva N, Amin S, Geacintov NE, Broyde S, Patel DJ. Solution conformation of the (-)-cis-anti-benzo[a]pyrenyl-dG adduct opposite dC in a DNA duplex: Intercalation of the covalently attached BP ring into the helix with base displacement of the modified deoxyguanosine into the major groove. Biochemistry. 35:1996;9850-9863.
20. 8-modified syn guanine and adjacent unpaired 3'-adenine into the major groove. Biochemistry. 34:1995;16641-16653.
21. Lilley DMJ. Kinking of DNA and RNA by base bulges. Proc Natl Acad Sci USA. 92:1995;7140-7142.
22. Huang H, Zhu L, Reid BR, Drobny GP, Hopkins PB. Solution structure of a cisplatin-induced DNA interstrand cross-link. Science. 270:1995;1842-1845.
23. Paquet F, Pérez C, Leng M, Lancelot G, Malinge JM. NMR solution structure of a DNA decamer containing an interstrand cross-link of the antitumor drug cis- diamminedichloroplatinum(II). J Biomol Struct Dyn. 14:1996;67-77.
24. Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD. Structure of a DNA - porphyrin complex. Biochemistry. 35:1996;2818-2823.
25. 2 triple helix fragments in a crystal structure. Science. 273:1996;1702-1705.
26. Liu K, Sasisekharan V, Miles HT, Raghunathan G. Structure of Py·Pu·Py DNA triple helices. Fourier transforms of fiber-type X-ray diffraction of single crystals. Biopolymers. 39:1996;573-589 Triple helices turn out to be remarkably difficult to crystallize. This paper presents the best analysis that can currently be carried out and discusses what may be behind the problems. of special interest.
27. Sun JS, Garestier G, Hélène C. Oligonucleotide directed triple helix formation. Curr Opin Struct Biol. 6:1996;327-333.
28. Kuryavyi VV, Jovin TM. Triad-DNA: a model for trinucleotide repeats. Nat Genet. 9:1995;339-341 This paper presents a novel and unusual proposition to explain the special properties of triplet repeats - a duplex containing base triplets. of special interest.
29. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. RNA tertiary mediation by adenosine platforms. Science. 273:1996;1696-1699.
30. Kettani A, Bouaziz S, Wang W, Jones RA, Patel DJ. Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triplets. Nat Struct Biol. 1997; Base triads cohabit with base tetrads within a complex structure formed by four pentanucleotides. of special interest.
31. 4 tetramer. J Mol Biol. 261:1996;399-414.
32. Lebrun A, Lavery R. Modeling a strand exchange tetraplex conformation. J Biomol Struct Dyn. 13:1995;459-464.
33. Kettani A, Kumar RA, Patel DJ. Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat. J Mol Biol. 254:1995;638-656.
34. Zhu L, Chou SH, Xu J, Reid BR. Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA. Nat Struct Biol. 2:1995;1012-1017.
35. n repeats form intramolecular hairpins stabilized by different base-pairing interactions. Biochemistry. 35:1995;13125-13135.
36. Chou S-H, Zhu L, Gao Z, Cheng J-W, Reid BR. Hairpin loops consisting of single adenine residues closed by sheared A·A and G·G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. J Mol Biol. 264:1996;981-1001.
37. Zhu L, Chou SH, Reid BR. A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins. Proc Natl Acad Sci USA. 93:1996;12159-12164 This study represents a good example of how DNA structure can become remarkably sensitive to base sequence modifications. The results may also have relevance to the structuring of human centromeres. of special interest.
38. Kuklenyik Z, Yao S, Marzilli LG. Similar conformations of hairpins with TTT and TTTT sequences. NMR and molecular modeling evidence for T·T base pairs in the TTTT hairpin. Eur J Biochem. 236:1996;960-969.
39. n. Nucleic Acids Res. 24:1996;784-792.
40. Yang D, Van Boom SSGE, Reedjik J, Van Boom JH, Farrell N, Wang AH-J. A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA. Nat Struct Biol. 2:1995;577-585.
41. Minyat EE, Khomyakova EB, Petrova MV, Zdobnov EM, Ivanov VI. Experimental evidence for slipped loop DNA a novel folding type for polynucleotide chain. J Biomol Struct Dyn. 13:1996;523-527.
42. Phe anticodon domain. Nat Struct Biol. 3:1996;38-44 Even if normal DNA does not create tertiary structures as complex as those of tRNA, this study shows that a limited number of modifications succeed in creating a stem-loop that looks sufficiently similar to the tRNA anticodon to be able to bind to the ribosome. of special interest.
43. Lin CH, Patel DJ. Encapsulating an amino acid in a DNA fold. Nat Struct Biol. 3:1996;1046-1050 The first solution structure of a steadily growing family of DNA aptamers. This case shows intricate recognition of an amino acid by a DNA stem-loop. of outstanding interest.
44. Nunn CM, Neidle S. The structure of chain-linked DNA as a possible model for the transcription bubble. Nat Struct Biol. 2:1995;1060-1061.
45. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, Chatenay D, Caron F. DNA: an extensible molecule. Science. 271:1996;792-794 How to trap a single DNA molecule and stretch it. Following the force versus extension curve shows that stretching induces a cooperative structural transition. of outstanding interest.
46. Smith SB, Cui Y, Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:1996;795-798 An alternative approach to the problem of stretching single DNA molecules. of outstanding interest.
47. Lebrun A, Lavery R. Modelling extreme stretching of DNA. Nucleic Acids Res. 24:1996;2260-2267 Molecular modelling provides a mechanism that explains how DNA can be stretched to more than twice its usual length before breaking, and it brings to light two new conformations for the double helix as a function of which ends of the helix are pulled: the ribbon; and the fibre. of special interest.
48. Konrad MW, Bolonick JI. Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure. J Am Chem Soc. 118:1996;10989-10994 MD simulations of DNA stretching, using an implicit solvent model, lead to a ribbon-like conformation. of special interest.
49. Strick T, Allemand JF, Bensimon D, Bensimon A, Croquette V. The elasticity of a single supercoiled DNA molecule. Science. 271:1996;1835-1837 These single molecule experiments allow an investigation of the elastic response of DNA to both positive and negative supercoiling. Beyond critical forces, both overwinding and underwinding lead to structural transitions. of special interest.
50. Liberles DA, Dervan PB. Design of artificial sequence-specific DNA binding ligands. Proc Natl Acad Sci USA. 93:1996;9510-9514 How to bend a DNA duplex using two triple helix forming oligonucleotides separated by a linker. of special interest.
51. Akiyama T, Hogan ME. The design of an agent to bend DNA. Proc Natl Acad Sci USA. 93:1996;12122-12127 The authors use a finer linker to bend one turn of duplex DNA and observe that bending towards the minor groove is surprisingly easy to achieve. of special interest.
52. Akiyama T, Hogan ME. Microscopic DNA flexibility analysis. J Biol Chem. 271:1996;29126-29135.
53. Strauss JK, Roberts C, Nelson MG, Switzer C, Maher LJ. DNA bending by hexamethylene-tethered ammonium ions. Proc Natl Acad Sci USA. 93:1996;9515-9520.
54. Travers AA. Reading the minor groove. Nat Struct Biol. 2:1995;615-618 This article contains an interesting suggestion concerning protein-induced DNA bending. In contrast to earlier phosphate neutralization models that bend DNA towards a protein, this idea invokes the low dielectric nature of the protein as a cause for increased phosphate - phosphate repulsion and bending away. of special interest.
55. Elcock AH, McCammon JA. The low dielectric interior of proteins is sufficient to cause major structural changes in DNA on association. J Am Chem Soc. 118:1996;3787-3788 MD simulations of DNA in the presence of a simple, low dielectric model of a protein confirm the mechanism of Travers [54]. of special interest.
56. Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan RG. A positively charged residue does not alter the bending of a DNA duplex. J Am Chem Soc. 118:1996;13073-13074.
57. Guzikevich-Guerstein G, Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nat Struct Biol. 3:1996;32-37 A new way to look at the TBP complex: bending is caused by junctions between flanking B-DNA segments and a new A-like DNA conformation induced by the protein that has strong positive base-pair inclination. of special interest.
58. Lebrun A, Shakked Z, Lavery R. Local DNA stretching reproduces unique features of the TATA box binding complex. Proc Natl Acad Sci USA. 1997; Molecular modelling provides a mechanism that explains how TBP can deform DNA upon binding and that also points to a relationship with the ribbon form of DNA obtained by stretching. of outstanding interest.
59. Werner MH, Gronenborn AM, Clore GM. Intercalation, DNA kinking, and the control of transcription. Science. 271:1996;778-784 An interesting summary of how and why protein sidechains invade the double helix, and what consequences these have. of special interest.
60. Qi J, Li X, Yang X, Seeman NC. Ligation of triangles built from bulged 3-arm DNA branched junctions. J Am Chem Soc. 118:1996;6121-6130.
61. Yang M, Millar DP. Conformational flexibility of three-way DNA junctions containing unpaired nucleotides. Biochemistry. 35:1996;7959-7967.
62. Li X, Yang X, Qi J, Seeman NC. Antiparallel DNA double crossover molecules as components for nanoconstruction. J Am Chem Soc. 118:1996;6131-6140.
63. Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW. Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science. 274:1996;415-421 RuvA and RuvB act together to drive branch migration of Holliday junctions. The crystal structure obtained for RuvA reveals a tetramer perfectly adapted to binding the square planar form of a four-arm junction. of outstanding interest.
64. Alivisatos AP, Johnsson KP, Peng X, Wilson TE, Loweth CJ, Bruchez MP, Schultz PG. Organization of 'nanocrystal molecules' using DNA. Nature. 382:1996;609-611 DNA is used here as a means for spatially positioning nanocrystals, prefiguring future uses of this macromolecule as a molecular construction tool. of special interest.
65. Tung CS, Soumpasis DM. The construction of DNA helical duplexes along prescribed 3-D curves. J Biomol Struct Dyn. 13:1995;577-582.
66. n: sequence elements responsible for curvature. Nucleic Acids Res. 24:1996;1632-1637.
67. Tung CS, Soumpasis DM. Structural prediction of A- and B-DNA duplexes based on coordinates of the phosphorus atoms. Biophys J. 70:1996;917-923.
68. Brown SC, Thompson SA, Veal JM, Davis DG. NMR solution structure of a peptide nucleic acid complexed with RNA. Science. 265:1994;777-780.